{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,10]],"date-time":"2026-11-10T17:57:16Z","timestamp":1794333436856,"version":"4.9.0"},"reference-count":58,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T00:00:00Z","timestamp":1776643200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"vor","delay-in-days":42,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2024YFE0199000"],"award-info":[{"award-number":["2024YFE0199000"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Hospital Development Center Foundation","award":["SHDC2022CRD041"],"award-info":[{"award-number":["SHDC2022CRD041"]}]},{"name":"Talent Program on Public Health System Construction of Shanghai","award":["GWV1-11.2-XD01"],"award-info":[{"award-number":["GWV1-11.2-XD01"]}]},{"name":"Talent Program on academic clinicians of Shanghai Jiao Tong University School of Medicine","award":["20240818"],"award-info":[{"award-number":["20240818"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32370186"],"award-info":[{"award-number":["32370186"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Genome Med"],"DOI":"10.1186\/s13073-026-01657-3","type":"journal-article","created":{"date-parts":[[2026,4,19]],"date-time":"2026-04-19T22:53:10Z","timestamp":1776639190000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["DposFinder: an interpretable transformer model for predicting phage-derived polysaccharide depolymerases and their host capsular serotypes"],"prefix":"10.1186","volume":"18","author":[{"given":"Yanxiang","family":"Shen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heyuan","family":"Lun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yumeng","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhikang","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cui","family":"Tai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohua","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiangning","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ping","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong-Yu","family":"Ou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,4,20]]},"reference":[{"key":"1657_CR1","doi-asserted-by":"publisher","first-page":"175","DOI":"10.3390\/antibiotics10020175","volume":"10","author":"G Topka-Bielecka","year":"2021","unstructured":"Topka-Bielecka G, Dydecka A, Necel A, Bloch S, Nejman-Fale\u0144czyk B, W\u0119grzyn G, et al. Bacteriophage-derived depolymerases against bacterial biofilm. Antibiotics. 2021;10:175.","journal-title":"Antibiotics"},{"key":"1657_CR2","doi-asserted-by":"crossref","unstructured":"Liston SD, McMahon SA, Le Bas A, Suits MD, Naismith JH, Whitfield C. Periplasmic depolymerase provides insight into ABC transporter-dependent secretion of bacterial capsular polysaccharides. Proceedings of the national academy of sciences. 2018;115:E4870-E4879.","DOI":"10.1073\/pnas.1801336115"},{"key":"1657_CR3","doi-asserted-by":"publisher","first-page":"2847","DOI":"10.1038\/s41564-024-01832-5","volume":"9","author":"B Gaborieau","year":"2024","unstructured":"Gaborieau B, Vaysset H, Tesson F, Charachon I, Dib N, Bernier J, et al. Prediction of strain level phage-host interactions across the Escherichia genus using only genomic information. Nat Microbiol. 2024;9:2847\u201361.","journal-title":"Nat Microbiol"},{"key":"1657_CR4","doi-asserted-by":"publisher","first-page":"5607","DOI":"10.1016\/S0021-9258(18)61851-4","volume":"246","author":"EC Yurewicz","year":"1971","unstructured":"Yurewicz EC, Ghalambor MA, Duckworth DH, Heath EC. Catalytic and molecular properties of a phage-induced capsular polysaccharide depolymerase. J Biol Chem. 1971;246:5607\u201316.","journal-title":"J Biol Chem"},{"key":"1657_CR5","doi-asserted-by":"publisher","first-page":"3","DOI":"10.3390\/antibiotics10010003","volume":"10","author":"C Uru\u00e9n","year":"2020","unstructured":"Uru\u00e9n C, Chopo-Escuin G, Tommassen J, Mainar-Jaime RC, Arenas J. Biofilms as promoters of bacterial antibiotic resistance and tolerance. Antibiotics. 2020;10:3.","journal-title":"Antibiotics"},{"key":"1657_CR6","doi-asserted-by":"publisher","first-page":"3103","DOI":"10.1007\/s00253-017-8224-6","volume":"101","author":"A Latka","year":"2017","unstructured":"Latka A, Maciejewska B, Majkowska-Skrobek G, Briers Y, Drulis-Kawa Z. Bacteriophage-encoded virion-associated enzymes to overcome the carbohydrate barriers during the infection process. Appl Microbiol Biotechnol. 2017;101:3103\u201319.","journal-title":"Appl Microbiol Biotechnol"},{"key":"1657_CR7","doi-asserted-by":"publisher","first-page":"198951","DOI":"10.1016\/j.virusres.2022.198951","volume":"322","author":"NV Volozhantsev","year":"2022","unstructured":"Volozhantsev NV, Borzilov AI, Shpirt AM, Krasilnikova VM, Verevkin VV, Denisenko EA, et al. Comparison of the therapeutic potential of bacteriophage KpV74 and phage-derived depolymerase (\u03b2-glucosidase) against Klebsiella pneumoniae capsular type K2. Virus Res. 2022;322:198951.","journal-title":"Virus Res"},{"key":"1657_CR8","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1016\/j.virs.2022.04.005","volume":"37","author":"M Li","year":"2022","unstructured":"Li M, Wang H, Chen L, Guo G, Li P, Ma J, et al. Identification of a phage-derived depolymerase specific for KL47 capsule of Klebsiella pneumoniae and its therapeutic potential in mice. Virol Sin. 2022;37:538\u201346.","journal-title":"Virol Sin"},{"key":"1657_CR9","doi-asserted-by":"publisher","first-page":"732","DOI":"10.3390\/antibiotics9110732","volume":"9","author":"V Volozhantsev","year":"2020","unstructured":"Volozhantsev V, Shpirt NM, Borzilov AI, Komisarova AV, Krasilnikova EM, Shashkov VS. Characterization and therapeutic potential of bacteriophage-encoded polysaccharide depolymerases with \u03b2 galactosidase activity against Klebsiella pneumoniae K57 capsular type. Antibiotics. 2020;9:732.","journal-title":"Antibiotics"},{"key":"1657_CR10","doi-asserted-by":"publisher","first-page":"545","DOI":"10.3389\/fmicb.2019.00545","volume":"10","author":"Y Liu","year":"2019","unstructured":"Liu Y, Leung SSY, Guo Y, Zhao L, Jiang N, Mi L, et al. The capsule depolymerase Dpo48 rescues Galleria mellonella and mice from Acinetobacter baumannii systemic infections. Front Microbiol. 2019;10:545.","journal-title":"Front Microbiol"},{"key":"1657_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12866-015-0455-z","volume":"15","author":"S Bansal","year":"2015","unstructured":"Bansal S, Harjai K, Chhibber S. Aeromonas punctata derived depolymerase improves susceptibility of Klebsiella pneumoniae biofilm to gentamicin. BMC Microbiol. 2015;15:1\u201310.","journal-title":"BMC Microbiol"},{"key":"1657_CR12","doi-asserted-by":"publisher","first-page":"845500","DOI":"10.3389\/fmicb.2022.845500","volume":"13","author":"X Chen","year":"2022","unstructured":"Chen X, Liu M, Zhang P, Xu M, Yuan W, Bian L, et al. Phage-derived depolymerase as an antibiotic adjuvant against multidrug-resistant Acinetobacter baumannii. Front Microbiol. 2022;13:845500.","journal-title":"Front Microbiol"},{"key":"1657_CR13","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1016\/j.virusres.2017.09.026","volume":"243","author":"EV Solovieva","year":"2018","unstructured":"Solovieva EV, Myakinina VP, Kislichkina AA, Krasilnikova VM, Verevkin VV, Mochalov VV, et al. Comparative genome analysis of novel Podoviruses lytic for hypermucoviscous Klebsiella pneumoniae of K1, K2, and K57 capsular types. Virus Res. 2018;243:10\u20138.","journal-title":"Virus Res"},{"key":"1657_CR14","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1186\/s13073-016-0294-z","volume":"8","author":"A Langdon","year":"2016","unstructured":"Langdon A, Crook N, Dantas G. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Med. 2016;8:39.","journal-title":"Genome Med"},{"key":"1657_CR15","doi-asserted-by":"publisher","first-page":"112048","DOI":"10.1016\/j.celrep.2023.112048","volume":"42","author":"B Beamud","year":"2023","unstructured":"Beamud B, Garcia-Gonzalez N, Gomez-Ortega M, Gonzalez-Candelas F, Domingo-Calap P, Sanjuan R. Genetic determinants of host tropism in Klebsiella phages. Cell Rep. 2023;42:112048.","journal-title":"Cell Rep"},{"key":"1657_CR16","doi-asserted-by":"publisher","first-page":"2649","DOI":"10.3389\/fmicb.2019.02649","volume":"10","author":"A Latka","year":"2019","unstructured":"Latka A, Leiman PG, Drulis-Kawa Z, Briers Y. Modeling the architecture of depolymerase-containing receptor binding proteins in Klebsiella phages. Front Microbiol. 2019;10:2649.","journal-title":"Front Microbiol"},{"key":"1657_CR17","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1186\/s12859-023-05341-w","volume":"24","author":"DJ Magill","year":"2023","unstructured":"Magill DJ, Skvortsov TA. DePolymerase Predictor (DePP): a machine learning tool for the targeted identification of phage depolymerases. BMC Bioinformatics. 2023;24:208.","journal-title":"BMC Bioinformatics"},{"key":"1657_CR18","doi-asserted-by":"publisher","first-page":"109836","DOI":"10.1016\/j.compbiomed.2025.109836","volume":"188","author":"MF Vieira","year":"2025","unstructured":"Vieira MF, Duarte J, Domingues R, Oliveira H, Dias O. PhageDPO: a machine-learning based computational framework for identifying phage depolymerases. Comput Biol Med. 2025;188:109836.","journal-title":"Comput Biol Med"},{"key":"1657_CR19","doi-asserted-by":"publisher","first-page":"giae017","DOI":"10.1093\/gigascience\/giae017","volume":"13","author":"Y Yang","year":"2024","unstructured":"Yang Y, Dufault-Thompson K, Yan W, Cai T, Xie L, Jiang X. Large-scale genomic survey with deep learning-based method reveals strain-level phage specificity determinants. GigaScience. 2024;13:giae017.","journal-title":"GigaScience"},{"key":"1657_CR20","doi-asserted-by":"publisher","first-page":"e1011831","DOI":"10.1371\/journal.pcbi.1011831","volume":"20","author":"R Concha-Eloko","year":"2024","unstructured":"Concha-Eloko R, Stock M, De Baets B, Briers Y, Sanjuan R, Domingo-Calap P, et al. DepoScope: accurate phage depolymerase annotation and domain delineation using large language models. PLoS Comput Biol. 2024;20:e1011831.","journal-title":"PLoS Comput Biol"},{"key":"1657_CR21","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","volume":"28","author":"L Fu","year":"2012","unstructured":"Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150\u20132.","journal-title":"Bioinformatics"},{"key":"1657_CR22","first-page":"2825","volume":"12","author":"F Pedregosa","year":"2011","unstructured":"Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, et al. Scikit-learn: machine learning in python. J Mach Learn Res. 2011;12:2825\u201330.","journal-title":"J Mach Learn Res"},{"key":"1657_CR23","doi-asserted-by":"publisher","first-page":"1123","DOI":"10.1126\/science.ade2574","volume":"379","author":"Z Lin","year":"2023","unstructured":"Lin Z, Akin H, Rao R, Hie B, Zhu Z, Lu W, et al. Evolutionary-scale prediction of atomic-level protein structure with a language model. Science. 2023;379:1123\u201330.","journal-title":"Science"},{"key":"1657_CR24","unstructured":"Paszke A, Gross S, Massa F, Lerer A, Bradbury J, Chanan G et al. Pytorch: an imperative style, high-performance deep learning library. Adv Neural Inf Process Syst. 2019;32:8024\u20138035."},{"key":"1657_CR25","unstructured":"Chollet F, Keras. Available at: https:\/\/github.com\/fchollet\/keras. Accessed. 2015;12:2021."},{"key":"1657_CR26","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1631\/FITEE.1700813","volume":"19","author":"B Yu","year":"2018","unstructured":"Yu B, Kumbier K. Artificial intelligence and statistics. Front Inform Technol Electron Eng. 2018;19:6\u20139.","journal-title":"Front Inform Technol Electron Eng"},{"key":"1657_CR27","unstructured":"Van der Maaten L, Hinton G. Visualizing data using t-SNE. J Mach Learn Res. 2008;9:2579\u22122605."},{"key":"1657_CR28","doi-asserted-by":"crossref","unstructured":"Rao R, Bhattacharya N, Thomas N, Duan Y, Chen P, Canny J et al. Evaluating protein transfer learning with TAPE. Adv Neural Inf Process Syst. 2019;32:9689-9701.","DOI":"10.1101\/676825"},{"key":"1657_CR29","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","volume":"596","author":"J Jumper","year":"2021","unstructured":"Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596:583\u20139.","journal-title":"Nature"},{"key":"1657_CR30","first-page":"82","volume":"40","author":"WL DeLano","year":"2002","unstructured":"DeLano WL. Pymol: an open-source molecular graphics tool. CCP4 Newsl Protein Crystallogr. 2002;40:82\u201392.","journal-title":"CCP4 Newsl Protein Crystallogr"},{"key":"1657_CR31","doi-asserted-by":"publisher","unstructured":"HenikoffS, Henikoff JG. Amino acid substitution matrices from protein blocks. Proceedings of the national academy of sciences. Proc Natl Acad Sci USA. 1992;89:10915\u201310919. https:\/\/doi.org\/10.1073\/pnas.89.22.1091.","DOI":"10.1073\/pnas.89.22.1091"},{"key":"1657_CR32","doi-asserted-by":"publisher","first-page":"4355","DOI":"10.1038\/s41467-024-48675-6","volume":"15","author":"D Boeckaerts","year":"2024","unstructured":"Boeckaerts D, Stock M, Ferriol-Gonzalez C, Oteo-Iglesias J, Sanjuan R, Domingo-Calap P, et al. Prediction of Klebsiella phage-host specificity at the strain level. Nat Commun. 2024;15:4355.","journal-title":"Nat Commun"},{"key":"1657_CR33","doi-asserted-by":"publisher","first-page":"D756","DOI":"10.1093\/nar\/gkad979","volume":"52","author":"RH Wang","year":"2024","unstructured":"Wang RH, Yang S, Liu Z, Zhang Y, Wang X, Xu Z, et al. PhageScope: a well-annotated bacteriophage database with automatic analyses and visualizations. Nucleic Acids Res. 2024;52:D756\u201361.","journal-title":"Nucleic Acids Res"},{"key":"1657_CR34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-11-119","volume":"11","author":"D Hyatt","year":"2010","unstructured":"Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:1\u201311.","journal-title":"BMC Bioinformatics"},{"key":"1657_CR35","doi-asserted-by":"publisher","first-page":"798","DOI":"10.1016\/j.resmic.2011.06.010","volume":"162","author":"D Pires","year":"2011","unstructured":"Pires D, Sillankorva S, Faustino A, Azeredo J. Use of newly isolated phages for control of Pseudomonas aeruginosa PAO1 and ATCC 10145 biofilms. Res Microbiol. 2011;162:798\u2013806.","journal-title":"Res Microbiol"},{"key":"1657_CR36","doi-asserted-by":"publisher","first-page":"2565","DOI":"10.1099\/vir.0.067553-0","volume":"95","author":"Y Wang","year":"2014","unstructured":"Wang Y, Wang W, Lv Y, Zheng W, Mi Z, Pei G, et al. Characterization and complete genome sequence analysis of novel bacteriophage IME-EFm1 infecting Enterococcus faecium. J Gen Virol. 2014;95:2565\u201375.","journal-title":"J Gen Virol"},{"key":"1657_CR37","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/s44280-024-00038-y","volume":"2","author":"Y Pan","year":"2024","unstructured":"Pan Y, Chen H, Ma R, Wu Y, Lun H, Wang A, et al. A novel depolymerase specifically degrades the K62-type capsular polysaccharide of Klebsiella pneumoniae. One Health Adv. 2024;2:5.","journal-title":"One Health Adv"},{"key":"1657_CR38","doi-asserted-by":"publisher","first-page":"2768","DOI":"10.3389\/fmicb.2019.02768","volume":"10","author":"Y Wu","year":"2019","unstructured":"Wu Y, Wang R, Xu M, Liu Y, Zhu X, Qiu J, et al. A novel polysaccharide depolymerase encoded by the phage SH-KP152226 confers specific activity against multidrug-resistant Klebsiella pneumoniae via biofilm degradation. Front Microbiol. 2019;10:2768.","journal-title":"Front Microbiol"},{"key":"1657_CR39","doi-asserted-by":"publisher","first-page":"e05304","DOI":"10.1128\/spectrum.05304-22","volume":"11","author":"R Cai","year":"2023","unstructured":"Cai R, Ren Z, Zhao R, Lu Y, Wang X, Guo Z, et al. Structural biology and functional features of phage-derived depolymerase Depo32 on Klebsiella pneumoniae with K2 serotype capsular polysaccharides. Microbiol Spectr. 2023;11:e05304\u201305322.","journal-title":"Microbiol Spectr"},{"key":"1657_CR40","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/j.apsb.2023.08.017","volume":"14","author":"H Wang","year":"2024","unstructured":"Wang H, Liu Y, Bai C, Leung SSY. Translating bacteriophage-derived depolymerases into antibacterial therapeutics: challenges and prospects. Acta Pharm Sin B. 2024;14:155\u201369.","journal-title":"Acta Pharm Sin B"},{"key":"1657_CR41","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1007\/s40259-013-0081-y","volume":"28","author":"J Yan","year":"2014","unstructured":"Yan J, Mao J, Xie J. Bacteriophage polysaccharide depolymerases and biomedical applications. BioDrugs. 2014;28:265\u201374.","journal-title":"BioDrugs"},{"key":"1657_CR42","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1038\/s41579-018-0070-8","volume":"16","author":"FL Nobrega","year":"2018","unstructured":"Nobrega FL, Vlot M, de Jonge PA, Dreesens LL, Beaumont HJ, Lavigne R, et al. Targeting mechanisms of tailed bacteriophages. Nat Rev Microbiol. 2018;16:760\u201373.","journal-title":"Nat Rev Microbiol"},{"key":"1657_CR43","doi-asserted-by":"publisher","first-page":"7241","DOI":"10.1038\/s41467-022-34972-5","volume":"13","author":"R Ouyang","year":"2022","unstructured":"Ouyang R, Costa AR, Cassidy CK, Otwinowska A, Williams VCJ, Latka A, et al. High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers. Nat Commun. 2022;13:7241.","journal-title":"Nat Commun"},{"key":"1657_CR44","doi-asserted-by":"crossref","unstructured":"Ye T-J, Fung K-M, Lee I-M, Ko T-P, Lin C-Y, Wong C-L et al. Klebsiella pneumoniae K2 capsular polysaccharide degradation by a bacteriophage depolymerase does not require trimer formation. mBio. 2024;15:e0351923.","DOI":"10.1128\/mbio.03519-23"},{"key":"1657_CR45","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/s12929-022-00792-4","volume":"29","author":"IF Tu","year":"2022","unstructured":"Tu IF, Lin T-L, Yang F-L, Lee IM, Tu W-L, Liao J-H, et al. Structural and biological insights into Klebsiella pneumoniae surface polysaccharide degradation by a bacteriophage K1 lyase: implications for clinical use. J Biomed Sci. 2022;29:9.","journal-title":"J Biomed Sci"},{"key":"1657_CR46","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1016\/j.str.2020.04.015","volume":"28","author":"F Squeglia","year":"2020","unstructured":"Squeglia F, Maciejewska B, Latka A, Ruggiero A, Briers Y, Drulis-Kawa Z, et al. Structural and functional studies of a Klebsiella phage capsule depolymerase tailspike: mechanistic insights into capsular degradation. Structure. 2020;28:613\u201324. e614.","journal-title":"Structure"},{"key":"1657_CR47","doi-asserted-by":"publisher","first-page":"e01329","DOI":"10.1128\/mbio.01329-23","volume":"14","author":"B Maciejewska","year":"2023","unstructured":"Maciejewska B, Squeglia F, Latka A, Privitera M, Olejniczak S, Switala P, et al. Klebsiella phage KP34gp57 capsular depolymerase structure and function: from a serendipitous finding to the design of active mini-enzymes against K. pneumoniae. mBio. 2023;14:e01329\u201301323.","journal-title":"mBio"},{"key":"1657_CR48","doi-asserted-by":"publisher","first-page":"144","DOI":"10.3390\/antibiotics10020144","volume":"10","author":"J Li","year":"2021","unstructured":"Li J, Sheng Y, Ma R, Xu M, Liu F, Qin R, et al. Identification of a depolymerase specific for K64-serotype Klebsiella pneumoniae: potential applications in capsular typing and treatment. Antibiotics. 2021;10:144.","journal-title":"Antibiotics"},{"key":"1657_CR49","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2180-9-252","volume":"9","author":"DJ Lee","year":"2009","unstructured":"Lee DJ, Bingle LE, Heurlier K, Pallen MJ, Penn CW, Busby SJ, et al. Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains. BMC Microbiol. 2009;9:1\u201314.","journal-title":"BMC Microbiol"},{"key":"1657_CR50","doi-asserted-by":"crossref","unstructured":"Zhang Y-Z, Liu Y, Bai Z, Fujimoto K, Uematsu S, Imoto S. Zero-shot-capable identification of phage\u2013host relationships with whole-genome sequence representation by contrastive learning. Brief Bioinform. 2023;24:bbad239.","DOI":"10.1093\/bib\/bbad239"},{"key":"1657_CR51","doi-asserted-by":"crossref","unstructured":"Bouras G, Nepal R, Houtak G, Psaltis AJ, Wormald P-J, Vreugde S. Pharokka: a fast scalable bacteriophage annotation tool. Bioinformatics. 2022;39:btac776.","DOI":"10.1093\/bioinformatics\/btac776"},{"key":"1657_CR52","doi-asserted-by":"publisher","first-page":"1038","DOI":"10.1128\/AAC.03560-14","volume":"59","author":"Y-J Pan","year":"2015","unstructured":"Pan Y-J, Lin T-L, Lin Y-T, Su P-A, Chen C-T, Hsieh P-F, et al. Identification of capsular types in carbapenem-resistant Klebsiella pneumoniae strains by wzc sequencing and implications for capsule depolymerase treatment. Antimicrob Agents Chemother. 2015;59:1038\u201347.","journal-title":"Antimicrob Agents Chemother"},{"key":"1657_CR53","doi-asserted-by":"crossref","unstructured":"Heinzinger M, Weissenow K, Sanchez Joaquin G, Henkel A, Mirdita M, Steinegger M et al. Bilingual language model for protein sequence and structure. NAR Genomics Bioinf. 2024;6:lqae150.","DOI":"10.1093\/nargab\/lqae150"},{"key":"1657_CR54","unstructured":"Su J, Han C, Zhou Y, Shan J, Zhou X, Yuan F. Saprot: protein language modeling with structure-aware vocabulary. Bioinformatics. 2026;42:btaf654."},{"issue":"2007","key":"1657_CR55","first-page":"2026","volume":"2024","author":"C Martin","year":"2025","unstructured":"Martin C, Gitter A, Anantharaman K. Protein set transformer: a protein-based genome language model to power high diversity viromics. BioRxiv. 2025;2024(2007):2026\u2013605391.","journal-title":"BioRxiv"},{"key":"1657_CR56","doi-asserted-by":"crossref","unstructured":"Latka A, Lemire S, Grimon D, Dams D, Maciejewska B, Lu T et al. Engineering the modular receptor-binding proteins of Klebsiella phages switches their capsule serotype specificity. mBio. 2021;12:e00455-00421.","DOI":"10.1128\/mBio.00455-21"},{"key":"1657_CR57","doi-asserted-by":"crossref","unstructured":"Shen Y, Lun H, Zhang Y, Wang Z, Tai C, Chen X et al. Source code of DposFinder: an interpretable transformer model for predicting phage-derived polysaccharide depolymerases and their host capsular serotypes. GitHub. 2026. https:\/\/github.com\/shenyanxiang\/DposFinder.","DOI":"10.1186\/s13073-026-01657-3"},{"key":"1657_CR58","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.13310759","author":"Y Shen","year":"2026","unstructured":"Shen Y, Lun H, Zhang Y, Wang Z, Tai C, Chen X, et al. Dataset of DposFinder: an interpretable transformer model for predicting phage-derived polysaccharide depolymerases and their host capsular serotypes. Zenodo. 2026. https:\/\/doi.org\/10.5281\/zenodo.13310759.","journal-title":"Zenodo"}],"container-title":["Genome Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13073-026-01657-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13073-026-01657-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13073-026-01657-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T02:02:07Z","timestamp":1780279327000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s13073-026-01657-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,20]]},"references-count":58,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["1657"],"URL":"https:\/\/doi.org\/10.1186\/s13073-026-01657-3","relation":{},"ISSN":["1756-994X"],"issn-type":[{"value":"1756-994X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,20]]},"assertion":[{"value":"5 September 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 April 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 April 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"75"}}